release 0.25.1 (#788)

mikemhenry · web-flow · commit c2f3e70e1a5f · 2025-08-08T14:52:06.000-07:00
* release 0.25.1 * modify ci matrix to reflect modern times * remove old scipy pin * don't have a python 3.13 build working for pymbar3 * update to use quad instead of quadrature, see https://docs.scipy.org/doc/scipy-1.16.1/release/1.15.0-notes.html#expired-deprecations * fix bug with unpacking return values * fix DeprecationWarning * fix DeprecationWarning for pkg_resources * add note to changelog about DeprecationWarning fixes * tests expect a string not a Path * fix DeprecationWarning for warn * add scipy changes to release notes
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -28,18 +28,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
-        openmm: ["8.1.2", "8.2.0"]
+        python-version: ["3.11", "3.12", "3.13"]
+        openmm: ["8.2.0", "8.3.1"]
         os: [macOS-latest, ubuntu-latest]
         pymbar-version: ["4"]
         include:
           # Test newest python, openmm, and pymbar we support on windows
-          - openmm: "8.2"
-            python-version: "3.12"
+          - openmm: "8.3.1"
+            python-version: "3.13"
             os: windows-latest
             pymbar-version: "4"
           # Have one job test pymbar 3 support
-          - openmm: "8.2"
+          - openmm: "8.3.1"
             python-version: "3.12"
             os: ubuntu-latest
             pymbar-version: "3"
@@ -54,9 +54,8 @@ jobs:
           ulimit -a
 
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
-          micromamba-version: '2.0.0-0'
           environment-file: devtools/conda-envs/test_env.yaml
           environment-name: openmmtools-test
           create-args: >-
@@ -66,7 +65,6 @@ jobs:
           condarc: |
             channels:
               - conda-forge
-              - jaimergp/label/unsupported-cudatoolkit-shim
             
       - name: Install package
         run: |
diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -15,7 +15,7 @@ dependencies:
   - python
   - python
   - pyyaml
-  - scipy < 1.14
+  - scipy >=1.15.0
   - setuptools
   - sphinxcontrib-bibtex
   # Testing
diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -1,6 +1,15 @@
 Release History
 ***************
 
+0.25.1
+======
+
+This release fixes a bug where ``get_entropy()`` and ``get_enthalpy() `` would return an ``AttributeError`` when using ``pymbar4``.
+See `#757 <https://github.com/choderalab/openmmtools/issues/757>`_ for more details.
+This release fixes deprecation warnings for ``pkg_resources`` and ``warnings.warn``.
+Replaced ``scipy.integrate.quadrature`` with ``scipy.integrate.quad`` to enable ``scipy >= 1.15.0`` support.
+See `#788 <https://github.com/choderalab/openmmtools/pull/788>`_ for more details.
+
 0.25.0
 ======
 
diff --git a/openmmtools/alchemy/alchemy.py b/openmmtools/alchemy/alchemy.py
@@ -328,7 +328,7 @@ def get_alchemical_variable(self, variable_name):
             The value of the alchemical variable.
         """
         import warnings
-        warnings.warn('AlchemicalState.get_alchemical_variable is deprecated. '
+        warnings.warning('AlchemicalState.get_alchemical_variable is deprecated. '
                       'Use AlchemicalState.get_function_variable instead.')
         return super().get_function_variable(variable_name)
 
@@ -347,7 +347,7 @@ def set_alchemical_variable(self, variable_name, new_value):
 
         """
         import warnings
-        warnings.warn('AlchemicalState.get_alchemical_variable is deprecated. '
+        warnings.warning('AlchemicalState.get_alchemical_variable is deprecated. '
                       'Use AlchemicalState.get_function_variable instead.')
         super().set_function_variable(variable_name, new_value)
 
diff --git a/openmmtools/mcmc.py b/openmmtools/mcmc.py
@@ -720,7 +720,7 @@ def apply(self, thermodynamic_state, sampler_state, context_cache=None):
             except Exception as e:
                 # Catches particle positions becoming nan during integration.
                 # Return the exception message as a warning
-                warnings.warn(str(e))
+                warnings.warning(str(e))
                 restart = True
             else:
                 timer.stop("{}: step({})".format(move_name, self.n_steps))
diff --git a/openmmtools/multistate/multistateanalyzer.py b/openmmtools/multistate/multistateanalyzer.py
@@ -1203,7 +1203,7 @@ def __init__(self, *args, unbias_restraint=True, restraint_energy_cutoff='auto',
                  restraint_distance_cutoff='auto', n_equilibration_iterations=None, statistical_inefficiency=None, max_subset=100, **kwargs):
 
         # Warn that API is experimental
-        logger.warn('Warning: The openmmtools.multistate API is experimental and may change in future releases')
+        logger.warning('Warning: The openmmtools.multistate API is experimental and may change in future releases')
 
         # super() calls clear() that initialize the cached variables.
         super().__init__(*args, **kwargs)
diff --git a/openmmtools/multistate/multistatereporter.py b/openmmtools/multistate/multistatereporter.py
@@ -129,7 +129,7 @@ def __init__(self, storage, open_mode=None,
                  ):
 
         # Warn that API is experimental
-        logger.warn('Warning: The openmmtools.multistate API is experimental and may change in future releases')
+        logger.warning('Warning: The openmmtools.multistate API is experimental and may change in future releases')
 
         # Handle checkpointing
         if type(checkpoint_interval) != int:
@@ -1293,7 +1293,7 @@ def read_online_analysis_data(self, iteration, *keys: str):
                 base_warn += "\n\t{}per-iteration: {}".format(iteration_str, failure)
             for missing in collected_not_found:
                 base_warn += "\n\tMissing: {}".format(missing)
-            warnings.warn(base_warn, RuntimeWarning)
+            warnings.warning(base_warn, RuntimeWarning)
         return collected_variables
 
     def write_online_analysis_data(self, iteration: Union[int, None], **kwargs):
diff --git a/openmmtools/multistate/multistatesampler.py b/openmmtools/multistate/multistatesampler.py
@@ -197,7 +197,7 @@ def __init__(self, mcmc_moves=None, number_of_iterations=1,
                  locality=None):
 
         # Warn that API is experimental
-        logger.warn('Warning: The openmmtools.multistate API is experimental and may change in future releases')
+        logger.warning('Warning: The openmmtools.multistate API is experimental and may change in future releases')
 
         # Display cuda device in debug log
         self._display_cuda_devices()
diff --git a/openmmtools/multistate/utils.py b/openmmtools/multistate/utils.py
@@ -225,7 +225,7 @@ def get_equilibration_data(timeseries_to_analyze, fast=True, max_subset=1000):
     --------
     get_equilibration_data_per_sample
     """
-    warnings.warn("This function will be removed in future versions of YANK due to redundancy, "
+    warnings.warning("This function will be removed in future versions of YANK due to redundancy, "
                   "Please use the more general `get_equilibration_data_per_sample` function instead.")
     i_t, g_i, n_effective_i = get_equilibration_data_per_sample(timeseries_to_analyze, fast=fast, max_subset=max_subset)
     n_effective_max = n_effective_i.max()
diff --git a/openmmtools/states.py b/openmmtools/states.py
@@ -3014,7 +3014,7 @@ def _on_setattr_callback(self, composable_state, attribute_name, old_composable_
             import warnings
             old_signature = '_on_setattr(self, standard_system, attribute_name)'
             new_signature = old_signature[:-1] + ', old_composable_state)'
-            warnings.warn('The signature IComposableState.{} has been deprecated, '
+            warnings.warning('The signature IComposableState.{} has been deprecated, '
                           'and future versions of openmmtools will support only the '
                           'new one: {}.'.format(old_signature, new_signature))
         if change_standard_system:
diff --git a/openmmtools/storage/iodrivers.py b/openmmtools/storage/iodrivers.py
@@ -969,7 +969,7 @@ def _attempt_storage_read(self):
                 raise TypeError("Storage target on NetCDF file is of type {} but this driver is designed to handle "
                                 "type {}!".format(self._bound_target.getncattr('IODriver_Type'), self.dtype_string()))
         except AttributeError:
-            warnings.warn("This Codec cannot detect storage type from on-disk variable. .write() and .append() "
+            warnings.warning("This Codec cannot detect storage type from on-disk variable. .write() and .append() "
                           "operations will not work and .read() operations may work", RuntimeWarning)
 
     def _check_storage_mode(self, expected_mode):
diff --git a/openmmtools/testsystems.py b/openmmtools/testsystems.py
@@ -172,9 +172,14 @@ def get_data_filename(relative_path):
         Name of the file to load (with respect to the repex folder).
 
     """
+    # See https://importlib-resources.readthedocs.io/en/latest/migration.html#pkg-resources-resource-filename
+    import importlib
+    from contextlib import ExitStack
+    import atexit
+    file_manager = ExitStack()
+    atexit.register(file_manager.close)
 
-    from pkg_resources import resource_filename
-    fn = resource_filename('openmmtools', relative_path)
+    fn = str(file_manager.enter_context(importlib.resources.as_file(importlib.resources.files("openmmtools") / relative_path)))
 
     if not os.path.exists(fn):
         raise ValueError("Sorry! %s does not exist. If you just added it, you'll have to re-install" % fn)
@@ -4588,8 +4593,8 @@ def integrand_numpy(x, args):
         # Integrate the free energy of binding in unitless coordinate system.
         xmin = 0.15  # in units of sigma
         xmax = 6.0  # in units of sigma
-        from scipy.integrate import quadrature
-        [integral, abserr] = quadrature(integrand_numpy, xmin, xmax, args=[context], maxiter=500)
+        from scipy.integrate import quad
+        integral, _ = quad(integrand_numpy, xmin, xmax, args=[context])
         # correct for performing unitless integration
         integral = integral * (self.sigma ** 3)
 
diff --git a/openmmtools/utils/utils.py b/openmmtools/utils/utils.py
@@ -680,7 +680,7 @@ def deserialize(serialization):
     except AttributeError:
         raise ValueError('Cannot deserialize class {} without a __setstate__ method'.format(class_name))
     except KeyError as e:  # Key not found in options/variables -- backward compatibility for <=0.21.4
-        warnings.warn(f"Key {e} not found in {instance.__class__.__name__}.")
+        warnings.warning(f"Key {e} not found in {instance.__class__.__name__}.")
     return instance
 
 
